4JOB

Crystal structure of human lysophosphatidic acid phosphatase type 6 complexed with L-(+)-tartrate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.171 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structures and biochemical studies of human lysophosphatidic acid phosphatase type 6

Li, J.Dong, Y.Lu, X.Wang, L.Peng, W.Zhang, X.C.Rao, Z.

(2013) Protein Cell 4: 548-561

  • DOI: 10.1007/s13238-013-3031-z
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Lysophosphatidic acid (LPA) is an important bioactive phospholipid involved in cell signaling through Gprotein-coupled receptors pathways. It is also involved in balancing the lipid composition inside the cell, and modulates the function of lipid raf ...

    Lysophosphatidic acid (LPA) is an important bioactive phospholipid involved in cell signaling through Gprotein-coupled receptors pathways. It is also involved in balancing the lipid composition inside the cell, and modulates the function of lipid rafts as an intermediate in phospholipid metabolism. Because of its involvement in these important processes, LPA degradation needs to be regulated as precisely as its production. Lysophosphatidic acid phosphatase type 6 (ACP6) is an LPA-specific acid phosphatase that hydrolyzes LPA to monoacylglycerol (MAG) and phosphate. Here, we report three crystal structures of human ACP6 in complex with malonate, L-(+)-tartrate and tris, respectively. Our analyses revealed that ACP6 possesses a highly conserved Rossmann-foldlike body domain as well as a less conserved cap domain. The vast hydrophobic substrate-binding pocket, which is located between those two domains, is suitable for accommodating LPA, and its shape is different from that of other histidine acid phosphatases, a fact that is consistent with the observed difference in substrate preferences. Our analysis of the binding of three molecules in the active site reveals the involvement of six conserved and crucial residues in binding of the LPA phosphate group and its catalysis. The structure also indicates a water-supplying channel for substrate hydrolysis. Our structural data are consistent with the fact that the enzyme is active as a monomer. In combination with additional mutagenesis and enzyme activity studies, our structural data provide important insights into substrate recognition and the mechanism for catalytic activity of ACP6.


    Organizational Affiliation

    National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysophosphatidic acid phosphatase type 6
A
396Homo sapiensMutation(s): 0 
Gene Names: ACP6 (ACPL1, LPAP)
EC: 3.1.3.2
Find proteins for Q9NPH0 (Homo sapiens)
Go to Gene View: ACP6
Go to UniProtKB:  Q9NPH0
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TLA
Query on TLA

Download SDF File 
Download CCD File 
A
L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.171 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 44.319α = 90.00
b = 91.028β = 90.00
c = 104.959γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
HKL-2000data collection
HKL-2000data reduction
DENZOdata reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-03-18 
  • Released Date: 2013-07-10 
  • Deposition Author(s): Li, J.

Revision History 

  • Version 1.0: 2013-07-10
    Type: Initial release
  • Version 1.1: 2013-08-14
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description